My name is Stefanie. For nine years, I’ve worked as a technical assistant in a plant researcher lab in Germany. About three years ago, I started to learn Python (under Windows). Just for fun because I was bored. I wrote some small scripts for my private stuff and also some small tools for my work. I realized more and more how convenient it is, to know a programming language. Then, I started to write serious applications for my daily jobs. The programs are quite simple, but make my (and others) life much easier because there are customized for our tasks. Quite fast I decided to try out a Linux distribution. I tried few, but after I used Ubuntu, I immediately fell in love.
Ubuntu looks pretty and smart! Ubuntu is easy to use! Ubuntu gives me freedom! Ubuntu just works! Ubuntu comes with Python! Python rocks! Ubuntu is for free! Ubuntu is simply cool I switched completely to Ubuntu.
A few months ago I followed a discussion on the PyConDE (the first Python conference in Germany!) mailing list about the lack of women’s speakers at the coming conference. I offered them to give a talk about finding duplicate microscope images with Python. They accepted my talk (well, they didn’t have a big choice) and two days ago I spoke about my project. The conference was really great. I got a lot of feedback (incredible!) and had great discussions after (actually I was unable to eat anything during the breaks). I would like to show some of my tools, which are written in Python under Ubuntu. I’m doing this only for fun, it has become my passion. I hope that more and more women try out programming and Ubuntu. It’s really great! It’s even better than Latte Macchiato or shoes
The first story is about what I presented at the conference:
We are working with barley. Barley has an enemy. Mildew, powdery mildew. We’re studying barley – powdery mildew interactions. Therefore, we’re looking at microscopical images (Picture 1) which show green cells and inside a fungal structure, so-called haustoria.
Picture 1: A barley epidermis cell, inside a haustoria.
Our automated system takes pictures automatically to store and analyze them. From time to time, we have to control the robots and therefore to look at the images again. In Python I wrote an annotation tool (Picture 2), a kind of image browser, which allows the user to scroll easily over many pictures and annotate them.
Picture 2: Annotation tool written in Python under Ubuntu.
The annotation data are stored in a database and can be exported as table files (e.g. LibreOffice calc). The slides of my presentation (unfortunately in German) could be found here:
My other tools are mostly about DNA sequences (http://labtools.ipk-gatersleben.de/), e.g. sequence alignment, sequence parsing, sequence creation and finding RNAi off-targets effects (Pictures 3 and 4).
Picture 3: si-Fi, a Software for RNAi (RNA interference) off-target prediction.
Picture 4: Blaster, a Software for sequence alignments.
I won’t go to much in details, please check out the links if you want to know more:
My only wishes for Ubuntu are to have or help creating a womanlike Ubuntu Theme. I think and hope that this will attract more women. Otherwise Ubuntu is perfect for modern girls like us
Thanks to Stefanie for being our fifth participant in the Ubuntu Women Month of Making! Please visit the wiki page or read the announcement for more information about this competition. Entries are to be sent to competition at ubuntu-women.org and the deadline is
October 7th extended to October 14th!